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Tutorial 3 - Add first draft of an xarray integration tutorial #15

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Dec 1, 2024
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Tutorial 3 - Add first draft of an xarray integration tutorial #15

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eb710bb
Add pre-commit
maxrjones Nov 21, 2024
40401a8
Add xarray tutorial
maxrjones Nov 21, 2024
554d08f
Merge branch 'main' into add-xarray-tutorial
maxrjones Dec 1, 2024
46a7e95
Remove separate black pre-commit hook
maxrjones Dec 1, 2024
245aae1
Add projection explanation
maxrjones Dec 1, 2024
3c8561e
Specify data server
maxrjones Dec 1, 2024
7f703c0
Apply suggestion from code review
maxrjones Dec 1, 2024
4ec3c16
Remove outputs
maxrjones Dec 1, 2024
50c986d
Merge branch 'main' into add-xarray-tutorial
weiji14 Dec 1, 2024
f91d48d
Rename tut03_spec_xarray to tut03_spe_xarray
weiji14 Dec 1, 2024
4f24524
Reorder dependencies in environment.yml
weiji14 Dec 1, 2024
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -3,3 +3,6 @@

# Jupyter Notebook
.ipynb_checkpoints/

# Data
book/data.nc
56 changes: 56 additions & 0 deletions .pre-commit-config.yaml
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repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-docstring-first
- id: check-json
- id: check-yaml
- id: debug-statements
- id: mixed-line-ending

- repo: https://github.com/asottile/pyupgrade
rev: v3.19.0
hooks:
- id: pyupgrade
args:
- "--py38-plus"

- repo: https://github.com/psf/black
rev: 24.10.0
hooks:
- id: black

- repo: https://github.com/keewis/blackdoc
rev: v0.3.9
hooks:
- id: blackdoc

- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: "v0.7.2"
hooks:
- id: ruff
args: ["--fix"]
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Oh, and just on this pre-commit config, there's this comment at https://github.com/astral-sh/ruff-pre-commit/tree/v0.7.4?tab=readme-ov-file#using-ruff-with-pre-commit:

When running with --fix, Ruff's lint hook should be placed before Ruff's formatter hook, and before Black, isort, and other formatting tools, as Ruff's fix behavior can output code changes that require reformatting

So maybe best to put ruff-pre-commit before black? Or just rely on ruff-format and remove black.


- repo: https://github.com/pre-commit/mirrors-prettier
rev: v4.0.0-alpha.8
hooks:
- id: prettier

- repo: https://github.com/nbQA-dev/nbQA
rev: 1.8.7
hooks:
- id: nbqa-ruff
args: ["--fix"]
- id: nbqa-isort
args: ["--profile=black"]
additional_dependencies: [isort==5.6.4]
- id: nbqa-black
- id: nbqa-pyupgrade
args: ["--py37-plus"]

- repo: https://github.com/shellcheck-py/shellcheck-py
rev: v0.10.0.1
hooks:
- id: shellcheck
6,707 changes: 6,707 additions & 0 deletions book/tut03_spec_xarray.ipynb
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Was trying to put inline comments with gitnotebooks but hit into this error - #9 (comment), so will have to put these all in one go:

  1. Description in first few cells
This tutorial is part of the AGU2024 annual meeting GMT/PyGMT pre-conference workshop (PREWS9) Mastering Geospatial Visualizations with GMT/PyGMT

Conference: https://agu.confex.com/agu/agu24/meetingapp.cgi/Session/226736
GitHub: https://github.com/GenericMappingTools/agu24workshop
Website: https://www.generic-mapping-tools.org/agu24workshop
Recommended version: PyGMT v0.13.0 with GMT 6.5.0

Debating on whether all of this needs to be here (thinking of when this goes into the Jupyter Book)? I could put some of this into #12 perhaps?

  1. Typo grd_image - grdimage

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Was trying to put inline comments with gitnotebooks but hit into this error - #9 (comment)

Please see my comments in Issue #9.

  1. Description in first few cells
    Debating on whether all of this needs to be here (thinking of when this goes into the Jupyter Book)? I could put > some of this into Add getting started and installation instructions to the welcome page #12 perhaps?

Yeah, I was thinking about this, when adding this part at the beginning of tutorial 4. I like to see, that all JN or files share a consistent layout of the introduction cell and clearly state to what this JN or script belongs and for which version it should work. So, I feel it makes sense to add this part for all JN or files together within one PR. Do we plan to upload the final workshop to Zenodo? Then we can also add this as a new line later.

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6 changes: 6 additions & 0 deletions environment.yml
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Expand Up @@ -7,6 +7,12 @@ dependencies:
- jupyterlab=4.2.5
- pygmt=0.13.0
- python=3.12
# Xarray tutorial
- xarray=2024.10.0
- gcsfs=2024.10.0
- zarr=2.18.3
# Optional dependencies
- geopandas=1.0.1
- jupyter-book=1.0.2
# Optional dev dependencies
- pre-commit